DNA Folding Form

Users of this service are requested to cite:

M. Zuker
Mfold web server for nucleic acid folding and hybridization prediction.
Nucleic Acids Res. 31 (13), 3406-15, (2003)
[Abstract] [Full Text] [Supplementary Material] [Additional Information]

The free energies used are from the laboratory of John SantaLucia Jr.
An appropriate citation for these energy rules is:
SantaLucia, Jr (1998) A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics.
Proc. Natl. Acad. Sci. USA 95, 1460-1465. (Abstract)

For the salt correction, please cite:
Peyret, N. (2000) Prediction of Nucleic Acid Hybridization: Parameters and Algorithms PhD dissertation, Wayne State University, Department of Chemistry, Detroit, MI

   

Enter constraint information in the box at the right. (optional) You may:

  1. force bases i,i+1,...,i+k-1 to be double stranded by entering:
    F   i   0   k on 1 line in the constraint box.
  2. force consecutive base pairs i.j,i+1.j-1, ...,i+k-1.j-k+1 by entering:
    F   i   j   k on 1 line in the constraint box.
  3. force bases i,i+1,...,i+k-1 to be single stranded by entering:
    P   i   0   k on 1 line in the constraint box.
  4. prohibit the consecutive base pairs i.j,i+1.j-1, ...,i+k-1.j-k+1 by entering:
    P   i   j   k on 1 line in the constraint box.
  5. prohibit bases i to j from pairing with bases k to l by entering:
    P   i-j   k-l on 1 line in the constraint box.
Ionic conditions:
Units:
Correction type:

Your job can be processed while you wait (the default) or can be submitted for batch processing by pressing the button below. In this case, you will be notified at a later time that the job is finished. Please make sure your E-mail address is correct in the window below.

Current limits: 2400 bases for an immediate job, 2400 for batch.

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